Andreas Tille pushed to branch master at Debian Med / microbiomeutil
Commits: 3e2eb3e4 by Andreas Tille at 2019-12-11T08:42:54Z chimeraslayer: Depends: ncbi-blast+-legacy - - - - - 5572fd8a by Andreas Tille at 2019-12-11T08:44:20Z nast-ier: Recommends: ncbi-blast+ - - - - - 2d9a8b93 by Andreas Tille at 2019-12-11T08:46:27Z routine-update: debhelper-compat 12 - - - - - 51a049f4 by Andreas Tille at 2019-12-11T08:46:33Z routine-update: Standards-Version: 4.4.1 - - - - - 053ee09c by Andreas Tille at 2019-12-11T08:46:34Z routine-update: Secure URI in copyright format - - - - - e345447e by Andreas Tille at 2019-12-11T08:46:34Z R-U: Trailing whitespace in debian/changelog - - - - - 947f9c71 by Andreas Tille at 2019-12-11T08:46:34Z R-U: Trailing whitespace in debian/control - - - - - dbc45034 by Andreas Tille at 2019-12-11T08:46:34Z R-U: autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g - - - - - b6de9d53 by Andreas Tille at 2019-12-11T08:49:59Z Fix also Build-Depends - - - - - 68a8d68e by Andreas Tille at 2019-12-11T08:56:34Z Upload to unstable - - - - - 5 changed files: - debian/changelog - − debian/compat - debian/control - debian/copyright - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,17 @@ +microbiomeutil (20101212+dfsg1-3) unstable; urgency=medium + + * chimeraslyer: Depends: ncbi-blast+-legacy + Closes: #946537 + * nast-ier: Recommends: ncbi-blast+ + * debhelper-compat 12 + * Standards-Version: 4.4.1 + * Secure URI in copyright format + * Remove trailing whitespace in debian/changelog + * Remove trailing whitespace in debian/control + * autopkgtest: s/ADTTMP/AUTOPKGTEST_TMP/g + + -- Andreas Tille <[email protected]> Wed, 11 Dec 2019 09:50:55 +0100 + microbiomeutil (20101212+dfsg1-2) unstable; urgency=low [ Steffen Moeller ] @@ -42,7 +56,7 @@ microbiomeutil (20101212+dfsg-1) unstable; urgency=low microbiomeutil (20101212-1ubuntu8) precise; urgency=low - * Bio-Linux rebuild with Andreas' fixes + * Bio-Linux rebuild with Andreas' fixes * ChimeraSlayer run from QIIME was not working. Need to pre-compute index files and add them to RESOURCES directory * Also added missing direct dep on blast2 @@ -80,7 +94,7 @@ microbiomeutil (20101212-2) unstable; urgency=low microbiomeutil (20101212-1ubuntu6) lucid; urgency=low * Another patch needed to Perl code due to inappropriate use of - FindBin + FindBin * Move to /usr/lib rather than /usr/share as per Lintian warnings. * Set --with quilt on dh. (Possibly not needed now?) * Added better descriptions in debian/control ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -4,10 +4,10 @@ Uploaders: Steffen Moeller <[email protected]>, Andreas Tille <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11~), +Build-Depends: debhelper-compat (= 12), cdbfasta, - blast2 -Standards-Version: 4.1.4 + ncbi-blast+-legacy +Standards-Version: 4.4.1 Vcs-Browser: https://salsa.debian.org/med-team/microbiomeutil Vcs-Git: https://salsa.debian.org/med-team/microbiomeutil.git Homepage: http://microbiomeutil.sourceforge.net/ @@ -32,7 +32,7 @@ Architecture: all Depends: ${misc:Depends}, microbiomeutil-data, cdbfasta, - blast2 + ncbi-blast+-legacy Recommends: nast-ier Description: detects likely chimeras in PCR amplified DNA ChimeraSlayer is a chimeric sequence detection utility, compatible with @@ -64,11 +64,12 @@ Depends: ${misc:Depends}, ${shlibs:Depends}, microbiomeutil-data, cdbfasta +Recommends: ncbi-blast+ Description: NAST-based DNA alignment tool - The NAST-iEr alignment utility aligns a single raw nucleotide sequence + The NAST-iEr alignment utility aligns a single raw nucleotide sequence against one or more NAST formatted sequences. . - The alignment algorithm involves global dynamic programming profile + The alignment algorithm involves global dynamic programming profile alignment to fixed (NAST-formatted) multiply aligned template sequences without any end-gap penalty. . ===================================== debian/copyright ===================================== @@ -1,4 +1,4 @@ -Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ +Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Contact: Brian J. Haas <[email protected]> Source: http://microbiomeutil.sourceforge.net/ Files-Excluded: ===================================== debian/tests/run-unit-test ===================================== @@ -1,10 +1,10 @@ #!/bin/sh -e pkg=microbiomeutil-data -if [ "$ADTTMP" = "" ] ; then - ADTTMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` +if [ "$AUTOPKGTEST_TMP" = "" ] ; then + AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXXXX` fi -cd $ADTTMP +cd $AUTOPKGTEST_TMP cp -a /usr/share/doc/${pkg}/examples/* . find . -name "*.gz" -exec gunzip \{\} \; for runtest in `find . -mindepth 1 -maxdepth 1 -type d` ; do View it on GitLab: https://salsa.debian.org/med-team/microbiomeutil/compare/f456ada47a6e308830b35fd6f7cea8539b57d789...68a8d68ef50c798979fffcac34cb8347775a4283 -- View it on GitLab: https://salsa.debian.org/med-team/microbiomeutil/compare/f456ada47a6e308830b35fd6f7cea8539b57d789...68a8d68ef50c798979fffcac34cb8347775a4283 You're receiving this email because of your account on salsa.debian.org.
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